Plot hole: The timing in the film is way off. Given the hours when JM Inc is open, most of the people there would only get to be Malkovich while he was asleep (yes, films have late-night shootings, but not every night); and Craig and Maxine stay up the whole time, then mess with Malkovich afterwards, then get in for work the following morning without showing any sign of fatigue even though there are less than 2 hours left for sleep.
Plot hole: After the scene of Rachel as a child, there are six days worth of events in what should be five days. Monday Lisa kills herself. Rachel works at photo hut. Tuesday Jesse and Tracy have sex, Walter is hit by car. Wednesday Rachel stands Jesse up because Mark and Eric have come to her house. Thursday Jesse and Rachel's first date - no sex. Thursday again Eric meets with the DA and Jesse and Rachel have sex. Friday is the game and party.
Plot hole: At the end when the gang get home to Andy's room, it's night time and the luggage trolley they drove home in is outside the neighbour's house. The next morning it's still there. But we see an ad with the 'chicken man' looking very sad because he lost Woody and the others. How could he have gone to Tokyo, realised the dolls were missing, then zoomed back to Tri County to do the ad the next day? While saving Woody, the toys explicitly say that Andy is returning home the following morning. They must have made it in one night, or they would have missed Andy's return.
Plot hole: If the Medjai are supposed to be the guardians against Imhotep and sworn to make sure he never comes back to life then why weren't they in possession of the key that opened everything in the first place?
Suggested correction: Because it got lost in the centuries that passed. It's possible they don't even know every step on how the mummy can return.